The use of mass spectrometry (MS) techniques has become invaluable across many fields where detailed analysis of various chemical, and often biological, samples is required. Such mass spectrometry analysis is used to identify the chemical makeup of given samples.
Straightforward analysis in a mass spectrometer typically involves the generation of ions from a chemical sample. The mass-to-charge ratio (m/z) and abundance of these ions are then measured by the mass spectrometer to produce a mass spectrum. The peaks (or centroids) in intensity at particular m/z values in such a mass spectrum provides a signature that indicates the relative abundance and mass of respective ions. This signature allows the compound (or compounds) that make up the original chemical sample to be identified.
For samples that comprise a large number of different compounds, such as biological samples, MS techniques are often combined with separation techniques. Separation techniques typically involve partitioning (or separation) of a sample, for example by washing a sample that is bound to a stationary phase with a solvent, such that various components of the sample are emitted from the sample as a function of a given separation parameter (or parameters) such as retention time. Common separation techniques include chromatography techniques—such as liquid chromatography (LC) or gas chromatography (GC). With combined chromatography and mass spectrometry techniques (such as LC/MS), the chromatographic technique causes different compounds (or analytes) to elute from the sample at different times (known as retention time) or, more typically, over a period of retention time. The compounds eluted at a given retention time are analysed using a mass spectrometer to produce a mass spectrum for that retention time. Thus, a typical chromatography/mass spectrometry analysis produces many individual mass spectra over a given period of retention time. These mass spectra vary as a function of retention time, indicating the variation of compounds eluted from the sample over the same time.
Analysis of these mass spectra as a function of the elution parameter allows not only individual eluted compounds to be identified, but also the sample as a whole to be identified or characterized. The elution parameter is typically retention time in the examples discussed above but may also be ion mobility, pH, ion size and/or other physio-chemical properties. Often such physio-chemical properties are proportional to the retention time. Typically, this analysis is done by generating mass traces (such as extracted ion chromatograms) for m/z values of interest. The m/z values of interest are themselves often determined based on the mass spectra. For example the m/z value of any intensity peak (in a spectrum) whose intensity falls above a certain threshold may be considered an m/z value of interest. A given mass trace is formed of the intensities of peaks in the mass spectra at (or around) a given m/z value. These intensities are then plotted as a function of elution parameter. A mass trace having a maximum (and optionally fulfilling certain other criteria such as a minimum abundance and or conformance to an expected signal model) is considered an event (or feature) and such a feature can be used in identifying a particular eluted compound.
The number of individual mass spectra produced by such combined separation/mass spectrometry techniques is often very large (for a typical LC/MS analysis it can be of the order of thousands of mass spectra). This means, in turn the number of mass traces identified is often correspondingly large (e.g. of the order of around 1,000 to 1,000,000 mass traces). Given this, the generation of mass traces typically requires automation.
The existing method for generating mass traces uses a pre-defined m/z window that is measured during elution. This is a range of m/z values, typically, centred on the m/z value of interest and any intensity peak in the mass spectra falling within this m/z window forms part of the mass trace for that m/z value. The window width is usually specified by a user or software designer, and must be adjusted by hand in the event of any errors in the mass trace generation. Automated determination of parameters (such as chromatographic peak width and its time dependence) is known from U.S. Pat. No. 9,395,341, but still uncommon.